EBV-encoded microRNAs (miRNAs) have been identified and their functions are being studied. The expression pattern of these miRNAs in clinical samples of EBV-associated nonHodgkin's lymphomas is unknown. We analyzed five primary ''endemic'' pediatric Burkitt's lymphomas (BL), two acquired immunodeficiency syndrome (AIDS)-related type I latency BL lines, a type III latency line, three EBV + primary effusion lymphomas (PEL), and three AIDS-related diffuse large B-cell lymphomas (DLBCL) for expression of EBV-encoded miRNAs.

We recently proposed that a nontemplate strand base in the discriminator region of bacterial promoters, the region between the ؊10 element and the transcription start site, makes sequence-specific contacts to region 1.2 of the subunit of Escherichia coli RNA polymerase (RNAP). Because rRNA promoters contain sequences within the discriminator region that are suboptimal for interaction with 1.2, these promoters have the kinetic properties required for regulation by the RNAP-binding factors DksA and ppGpp. Here, we use zero-length cross-linking and mutational, kinetic, and footprinting studies to map RNAP interactions with the nontemplate strand bases at the junction of the ؊10 element and the discriminator region in an unregulated rRNA promoter variant and in the PR promoter. Our studies indicate that nontemplate strand bases adjacent to the ؊10 element bind within a 9-aa interval in 1.2 (residues 99 -107). We also demonstrate that the downstream-most base on the nontemplate strand of the ؊10 hexamer cross-links to region 2, and not to 1.2. Our results refine models of RNAP-DNA interactions in the promoter complex that are crucial for regulation of transcription initiation.promoter element ͉ RNA polymerase ͉ transcription initiation ͉ discriminator region ͉ Ϫ10 element I nteractions between bacterial RNA polymerase holoenzyme (RNAP; ␣ 2 ␤␤Ј ) and the promoter can determine not only its basal strength but also its regulation. (In this report, always refers to 70 , the major factor.) Four promoter elements are generally recognized as making sequence-specific contacts with RNAP (1, 2) ( Fig. 1): the UP element (bound by the C-terminal domains of the two ␣ subunits); the Ϫ35 hexamer (bound by region 4.2); the extended Ϫ10 element (bound by region 3.0); and the Ϫ10 hexamer (bound by region 2.3-2.4). Recently, an additional element immediately downstream of the Ϫ10 hexamer, within the discriminator region, was proposed to bind to region 1.2 (3, 4).The term ''discriminator'' was coined by Travers (5) more than 25 years ago to describe a GϩC-rich region downstream from the Ϫ10 hexamer in stable RNA (rRNA and tRNA) promoters, and it was proposed that the GϩC content of this region was important for maintaining proper regulation of stable RNA promoters (6, 7). High GϩC content was proposed to impede strand separation, leading to promoter regulation. However, it was found that a C to G substitution 2 nt downstream from the Ϫ10 hexamer in the rRNA promoter rrnB P1 (rrnB P1 C-7G) eliminated its regulation, suggesting that the actual sequence of the discriminator region, in addition to its high GϩC content, is crucial for control of transcription (3).Footprinting, photocross-linking, and genetic approaches led to the conclusion that the nontemplate strand base two positions downstream from the Ϫ10 element in the rrnB P1 C-7G promoter contacts 1.2. When the base at the analogous position in all other promoters investigated was a C (either naturally or by mutation), competitor-resistant complexes formed with RNAP were much shorte...

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Supplementary Table 1 from EBV MicroRNAs in Primary Lymphomas and Targeting of <i>CXCL-11</i> by ebv-mir-BHRF1-3

<div>Abstract<p>EBV-encoded microRNAs (miRNAs) have been identified and their functions are being studied. The expression pattern of these miRNAs in clinical samples of EBV-associated non–Hodgkin's lymphomas is unknown. We analyzed five primary “endemic” pediatric Burkitt's lymphomas (BL), two acquired immunodeficiency syndrome (AIDS)-related type I latency BL lines, a type III latency line, three EBV⁺ primary effusion lymphomas (PEL), and three AIDS-related diffuse large B-cell lymphomas (DLBCL) for expression of EBV-encoded miRNAs. A markedly elevated expression of miRNA BHRF1-3 in type III relative to its parental type I BL line was found. Primary unmanipulated type I BLs and EBV⁺ PELs expressed high levels of BART2 miRNA, whereas DLBCLs expressed both BART2 and BHRF1-3 species. BHRF1-3 miRNA expression inversely correlated with levels of a putative cellular target, the IFN-inducible T-cell attracting chemokine <i>CXCL-11/I-TAC</i>, and suppression of this factor was reversed by transfection of an antisense oligo to the EBV miRNA BHRF1-3. EBV-encoded miRNAs are expressed in primary lymphomas classically linked to the virus and are associated with the viral latency status. Targeted suppression of <i>CXCL-11/I-TAC</i> by a viral-encoded miRNA may serve as an immunomodulatory mechanism in these tumors. [Cancer Res 2008;68(5):1436–42]</p></div>

<div>Abstract<p>EBV-encoded microRNAs (miRNAs) have been identified and their functions are being studied. The expression pattern of these miRNAs in clinical samples of EBV-associated non–Hodgkin's lymphomas is unknown. We analyzed five primary “endemic” pediatric Burkitt's lymphomas (BL), two acquired immunodeficiency syndrome (AIDS)-related type I latency BL lines, a type III latency line, three EBV⁺ primary effusion lymphomas (PEL), and three AIDS-related diffuse large B-cell lymphomas (DLBCL) for expression of EBV-encoded miRNAs. A markedly elevated expression of miRNA BHRF1-3 in type III relative to its parental type I BL line was found. Primary unmanipulated type I BLs and EBV⁺ PELs expressed high levels of BART2 miRNA, whereas DLBCLs expressed both BART2 and BHRF1-3 species. BHRF1-3 miRNA expression inversely correlated with levels of a putative cellular target, the IFN-inducible T-cell attracting chemokine <i>CXCL-11/I-TAC</i>, and suppression of this factor was reversed by transfection of an antisense oligo to the EBV miRNA BHRF1-3. EBV-encoded miRNAs are expressed in primary lymphomas classically linked to the virus and are associated with the viral latency status. Targeted suppression of <i>CXCL-11/I-TAC</i> by a viral-encoded miRNA may serve as an immunomodulatory mechanism in these tumors. [Cancer Res 2008;68(5):1436–42]</p></div>

Adult T-cell leukemia (ATL) is a lymphoid malignancy caused by the human T-cell leukemia virus type I (HTLV-I), which carries a poor prognosis. A hallmark of ATL is the high constitutive expression of NF-κB, which predominantly exerts an anti-apoptotic effect contributing to chemotherapy resistance. Many of the elegant studies about the pathogenesis of ATL have focused on Tax, a viral transactivator of NF-κB, using HTLV-I expressing cell lines and mouse models, however in primary tumors the virus remains latent and Tax is not detected. We and other investigators have demonstrated the clinical efficacy of Zidovudine (AZT) and interferon-alpha (IFNα) combination therapy in both chronic and acute ATL subtypes with some patients achieving clinical remission or stable disease for many years while on maintenance therapy. The exact mechanisms of these antiviral drugs in ATL remain unclear. In a recent analysis of primary ATL tumors, we implicated the expression of both c-Rel and the NF-κB target gene product IRF-4/MUM-1 in AZT/IFN resistant disease. We have recently opened to accrual a Phase II clinical trial titled Prospective Study of the Molecular Characteristics of Sensitive and Resistant Disease in Patients with HTLV-I Associated Adult T Cell Leukemia Treated with Zidovudine Plus Interferon alpha-2b, which includes the novel use of pegylated interferon-alpha and valproic acid (as HDAC inhibitor) in the maintenance phase as an attempt to eradicate residual ATL clones, which usually occurs after AZT and IFNα therapy even after longterm remission. Our goals are also to study the anti-tumor mechanisms of these drugs in ATL, and define molecular criteria for response. As part of the correlative studies in our Phase II trial, we have analyzed leukemic ATL cells collected from patients during the first 48 hours of treatment (AZT given alone prior to IFN) and found in vivo stabilization of IκB (the repressor protein of NF-κB) by Western Blot in patients responding to the treatment, suggesting a role for this antiviral drug in blocking NF-κB activity as previously hypothesized in our laboratory. We also examined the expression of NF-κB related genes using a custom designed gene expression array by a novel technology (NanoString Inc.) of selected NF-κB target genes and found downregulation of most these genes in vivo by AZT alone. So far, all ATL tumors analyzed exhibited high expression of many NF-κB target genes, and over forty of these are differentially overexpressed in ATL specimens as compared to normal CD4+ T-cells. Some the differentially expressed genes include those encoding NF-κB/Rel, interferon regulatory factor (IRF), and bcl-2 related proteins. A comprehensive analysis of over forty ATL tumors, including specimens collected in both Miami and Brazil, is ongoing and expected to be completed soon. Baseline tumor characteristics and prognostic variables of previously collected tumors, as well interim results of our clinical and molecular studies will be reported.

4877 Adult T-cell leukemia/lymphoma (ATLL) carries a dismal long-term prognosis and is generally chemotherapy resistant. We and other groups have demonstrated that the combination of AZT and interferon (IFN) alpha can effectively suppress ATLL long-term; however, these drugs fail to eradicate malignant ATLL clones as patients ultimately progress. We recently tested our hypothesis that histone deacelytase (HDAC) inhibitors would re-activate latent HTLV-I in ATLL cells harboring intact provirus thus helping to eliminate residual disease after cytoreductive treatment. Histone acetylation can result in HTLV-I promoter activation and viral transcription. We found that HDAC inhibitors, including the inexpensive drug valproic acid (VPA), reactivated HTLV-I expression in ATLL cells and caused apoptosis. Based on these concepts, we recently completed a pilot trial for ATLL using AZT/IFN and adding VPA during the maintenance treatment phase. Thirteen subjects with aggressive acute-type ATLL were enrolled in the study, including 11 treatment-naïve patients. The estimated 12-month overall survival rate was 46%. In 12 evaluable subjects (10 naïve) the complete response (CR) rate was 33% and overall response 42% (5 patients). A total of eight subjects (66%) had a hematologic response, including 5 complete hematologic responses (38%). VPA was added at the beginning of month 3 during AZT/IFN maintenance in 3 subjects. One subject achieved a molecular remission and clearance of ATLL after adding VPA as measured by serial multiplex PCR studies. This subject remains disease-free 2.5 years later. Our findings were surprising, as previous studies performed on long-term responders treated with AZT/IFN alone had not demonstrated any molecular remissions. Our data suggest that VPA could potentially eradicate ATLL clones in vivo. The dual anti-neoplastic and viral inducing roles of HDAC inhibitors can be exploited in the treatment of ATLL. This exciting approach may help advance the cure for this disease. We will present our updated interim clinical trial results at the conference. Disclosures: No relevant conflicts of interest to declare.